New insights into the novel sequences of the chicken pan-genome by liquid chip

文献类型： 外文期刊

第一作者： Wang, Fei

作者： Wang, Fei;Guo, Yingwei;Liu, Zhenyu;Jiang, Yu;Wang, Qiao;Zhao, Guiping

作者机构：

关键词： GWAS; liquid chip; novel sequence; pan-genome

期刊名称：JOURNAL OF ANIMAL SCIENCE （ 影响因子：3.338； 五年影响因子：3.243 ）

ISSN： 0021-8812

年卷期： 2022 年 100 卷 12 期

页码：

收录情况： SCI

摘要： Increasing evidence indicates that the missing sequences and genes in the chicken reference genome are involved in many crucial biological pathways, including metabolism and immunity. The low detection rate of novel sequences by resequencing hindered the acquisition of these sequences and the exploration of the relationship between new genes and economic traits. To improve the capture ratio of novel sequences, a 48K liquid chip including 25K from the reference sequence and 23K from the novel sequence was designed. The assay was tested on a panel of 218 animals from 5 chicken breeds. The average capture ratio of the reference sequence was 99.55%, and the average sequencing depth of the target sites was approximately 187X, indicating a good performance and successful application of liquid chips in farm animals. For the target region in the novel sequence, the average capture ratio was 33.15% and the average sequencing depth of target sites was approximately 60X, both of which were higher than that of resequencing. However, the different capture ratios and capture regions among varieties and individuals proved the difficulty of capturing these regions with complex structures. After genotyping, GWAS showed variations in novel sequences potentially relevant to immune-related traits. For example, a SNP close to the differentiation of lymphocyte-related gene IGHV3-23-like was associated with the H/L ratio. These results suggest that targeted capture sequencing is a preferred method to capture these sequences with complex structures and genes potentially associated with immune-related traits. Lay Summary A total of 48K target sites were selected to be placed on the liquid chip, including 23K from the novel sequence of the chicken pan-genome. The high average capture ratio (99.55%) of the reference sequence in five populations indicated the good performance of the liquid chip. For the target region in the novel sequence, the average capture ratio was approximately 33.15% and the average sequencing depth of target sites was approximately 60X, both of which were higher than that of resequencing. However, the capture ratio was different among varieties, ranging from 29.2% (White Leghorn) to 33.4% (B line). GWAS (Genome-wide association study) showed variations in novel sequences potentially related to immune-related traits. For example, an SNP (single nucleotide polymorphism) close to the differentiation of the lymphocyte-related gene IGHV3-23-like was associated with the H/L (heterophil/lymphocyte ratio) ratio. Overall, this study not only improved the capture ratio of regions with complex structures in novel sequences but also preliminarily explored the association of variations in these regions with chicken economic traits.

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